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Expanding the Repertoire of DNA-Mediated Signaling in DNA Repair


Mui, Timothy Paul (2014) Expanding the Repertoire of DNA-Mediated Signaling in DNA Repair. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/WXQM-CJ32.


DNA damage is extremely detrimental to the cell and must be repaired to protect the genome. DNA is capable of conducting charge through the overlapping π-orbitals of stacked bases; this phenomenon is extremely sensitive to the integrity of the π-stack, as perturbations attenuate DNA charge transport (CT). Based on the E. coli base excision repair (BER) proteins EndoIII and MutY, it has recently been proposed that redox-active proteins containing metal clusters can utilize DNA CT to signal one another to locate sites of DNA damage.

To expand our repertoire of proteins that utilize DNA-mediated signaling, we measured the DNA-bound redox potential of the nucleotide excision repair (NER) helicase XPD from Sulfolobus acidocaldarius. A midpoint potential of 82 mV versus NHE was observed, resembling that of the previously reported BER proteins. The redox signal increases in intensity with ATP hydrolysis in only the WT protein and mutants that maintain ATPase activity and not for ATPase-deficient mutants. The signal increase correlates directly with ATP activity, suggesting that DNA-mediated signaling may play a general role in protein signaling. Several mutations in human XPD that lead to XP-related diseases have been identified; using SaXPD, we explored how these mutations, which are conserved in the thermophile, affect protein electrochemistry.

To further understand the electrochemical signaling of XPD, we studied the yeast S. cerevisiae Rad3 protein. ScRad3 mutants were incubated on a DNA-modified electrode and exhibited a similar redox potential to SaXPD. We developed a haploid strain of S. cerevisiae that allowed for easy manipulation of Rad3. In a survival assay, the ATPase- and helicase-deficient mutants show little survival, while the two disease-related mutants exhibit survival similar to WT. When both a WT and G47R (ATPase/helicase deficient) strain were challenged with different DNA damaging agents, both exhibited comparable survival in the presence of hydroxyurea, while with methyl methanesulfonate and camptothecin, the G47R strain exhibits a significant change in growth, suggesting that Rad3 is involved in repairing damage beyond traditional NER substrates. Together, these data expand our understanding of redox-active proteins at the interface of DNA repair.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:XPD, Rad3, DNA-mediated Charge Transport, Nucleotide Excision Repair, Iron-Sulfur Cluster
Degree Grantor:California Institute of Technology
Division:Chemistry and Chemical Engineering
Major Option:Chemistry
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Barton, Jacqueline K.
Thesis Committee:
  • Gray, Harry B. (chair)
  • Campbell, Judith L.
  • Reisman, Sarah E.
  • Barton, Jacqueline K.
Defense Date:6 September 2013
Funding AgencyGrant Number
NSF Graduate Research FellowshipUNSPECIFIED
Record Number:CaltechTHESIS:09102013-094001578
Persistent URL:
Related URLs:
URLURL TypeDescription 2 5
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:7951
Deposited By: Timothy Mui
Deposited On:12 Sep 2013 16:38
Last Modified:08 Nov 2023 00:14

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